Hi Saira & Liubov,
On Fri, Jul 05, 2019 at 04:32:44PM +0200, Liubov Chuprikova wrote:
On Fri, 5 Jul 2019 at 15:15, Saira Hussain <saira.h0213@zoho.com> wrote:
My first step was to replicate some of the test suites inside Hyphy. In
order to do that I copied the SimpleAnalysis suite inside the tests and
configured them to run through autobuild.
There is no need to replicate files that are already inside the source
package. From this source, we are building three binary packages [1] and
one of them [2] contains all the files, you need for the tests. Just add
into run-unit-test a line to copy them to you temporary testing directory.
That's correct. If some files from the source distribution might be
needed for testing we can copy these into a dedicated data package - in
the hyphy case into hyphy-common where we have the examples directory
anyway.
[1] https://packages.debian.org/en/source/sid/hyphy
[2] https://packages.debian.org/sid/all/hyphy-common/filelist
@Liubov: Good hint to the filelist! (I was not aware of this and I love
to learn from my students!)
I had a *quick* look into the autopkgtest of hyphy. I pushed a fix
for a typo. When I now run the tests it starts nicely but than one
test seems to expect some user input:
...
3). 3 proportional equiprobable rates
R = 1.
Sample mean = 4.666666666666666 (sample variance = 16.33333333333333)
Rate[0]= 1.00000000 (weight=0.3333333)
Rate[1]= 4.00000000 (weight=0.3333333)
Rate[2]= 9.00000000 (weight=0.3333333)
------------------------------------------------
R = 5.
Sample mean = 23.33333333333333 (sample variance = 408.3333333333334)
Rate[0]= 5.00000000 (weight=0.3333333)
Rate[1]= 20.00000000 (weight=0.3333333)
Rate[2]= 45.00000000 (weight=0.3333333)
------------------------------------------------
4). User defined discrete distribution
Enter the number of categories: <<<<<================ here I just pressed enter
0 is an invalid number of categories
+ for i in *.bf
+ '[' -f definitions+MLE.bf ']'
+ hyphympi definitions+MLE.bf
Error:
Master node received an error:Could not read batch file '/tmp/hyphy-common-test.oGNZo5/displayfunction.bf'.
Path stack:
/usr/lib/hyphy/
/tmp/hyphy-common-test.oGNZo5/
/tmp/hyphy-common-test.oGNZo5/--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
@Saira: Please either patch the test to set some fixed
number or simply drop any test that might require user
interaction.